I used 4 PS3 controllers over bluetooth to run a Bomberman tournament at work on a Pi3 and it worked absolutely fine. Had it working with other games as well. Just remember some system require you to enable 'multi-tap' within RetroArch before the game will pick up the additional controllers.

I tested it with:

Bomberman on the SNES
Mario Kart 64
Micro Machines V3 (PS1)
Crash Team Racing (PS1)
Micro Machines Turbo Tournament (MegaDrive)

Hope this helps.

@TechieAndroid What was causing the games not to run? I'm having the same issue? Thanks.

@edmaul69 that's the problem. I did an update and forgot to add the bios, and had the exact same issue with CTR. Just add the bios and you will be racing!